Reshaping of sandstone surfaces by cryptoendolithic cyanobacteria: bioalkalization causes chemical weathering in arid landscapes

We report a novel weathering mechanism in South African sandstone formations, where cryptoendolithic cyanobacteria induce weathering by substrate alkalization during photosynthesis. As a result, the upper rock part is loosened and then eroded away by physical forces such as wind, water, trampling. This special type of ‘exfoliation’ is widely distributed and affects the geomorphology of whole sandstone mountain ranges and outcrops across several biomes. We show, that this weathering type is initiated by bioalkalization because of the photosynthesis of cryptoendolithic (i.e. those organisms living in small tight open spaces between the sand grains) cyanobacteria causing pH values high enough to enhance silica solution in the cryptoendolithic zone. As modern cyanobacteria are the initial photoautotrophic colonizers of bare rocks in arid and semiarid landscapes, it is possible that they may also have played a significant role in shaping sandstone landscapes in the geological past.     

The Primitive Thylakoid-Less Cyanobacterium Gloeobacter Is a Common Rock-Dwelling Organism

Cyanobacteria are an ancient group of photosynthetic prokaryotes, which are significant in biogeochemical cycles. The most primitive among living cyanobacteria, Gloeobacter violaceus, shows a unique ancestral cell organization with a complete absence of inner membranes (thylakoids) and an uncommon structure of the photosynthetic apparatus. Numerous phylogenetic papers proved its basal position among all of the organisms and organelles capable of plant-like photosynthesis (i.e., cyanobacteria, chloroplasts of algae and plants). Hence, G. violaceus has become one of the key species in evolutionary study of photosynthetic life. It also numbers among the most widely used organisms in experimental photosynthesis research. Except for a few related culture isolates, there has been little data on the actual biology of Gloeobacter, being relegated to an “evolutionary curiosity” with an enigmatic identity. Here we show that members of the genus Gloeobacter probably are common rock-dwelling cyanobacteria. On the basis of morphological, ultrastructural, pigment, and phylogenetic comparisons of available Gloeobacter strains, as well as on the basis of three new independent isolates and historical type specimen, we have produced strong evidence as to the close relationship of Gloeobacter to a long known rock-dwelling cyanobacterial morphospecies Aphanothece caldariorum. Our results bring new clues to solving the 40 year old puzzle of the true biological identity of Gloeobacter violaceus, a model organism with a high value in several biological disciplines. A probable broader distribution of Gloeobacter in common wet-rock habitats worldwide is suggested by our data, and its ecological meaning is discussed taking into consideration the background of cyanobacterial evolution. We provide observations of previously unknown genetic variability and phenotypic plasticity, which we expect to be utilized by experimental and evolutionary researchers worldwide.     

“Fish-in-Net”, a Novel Method for Cell Immobilization of Zymomonas mobilis

Background

Inorganic mesoporous materials exhibit good biocompatibility and hydrothermal stability for cell immobilization. However, it is difficult to encapsulate living cells under mild conditions, and new strategies for cell immobilization are needed. We designed a “fish-in-net” approach for encapsulation of enzymes in ordered mesoporous silica under mild conditions. The main objective of this study is to demonstrate the potential of this approach in immobilization of living cells.

Methodology/Principal Findings

Zymomonas mobilis cells were encapsulated in mesoporous silica-based materials under mild conditions by using a “fish-in-net” approach. During the encapsulation process, polyethyleneglycol was used as an additive to improve the immobilization efficiency. After encapsulation, the pore size, morphology and other features were characterized by various methods, including scanning electron microscopy, nitrogen adsorption-desorption analysis, transmission electron microscopy, fourier transform infrared spectroscopy, and elemental analysis. Furthermore, the capacity of ethanol production by immobilized Zymomonas mobilis and free Zymomonas mobilis was compared.

Conclusions/Significance

In this study, Zymomonas mobilis cells were successfully encapsulated in mesoporous silica-based materials under mild conditions by the “fish-in-net” approach. Encapsulated cells could perform normal metabolism and exhibited excellent reusability. The results presented here illustrate the enormous potential of the “fish-in-net” approach for immobilization of living cells.     

Endolithic chlorophyll d-containing phototrophs

Cyanobacteria in the genus Acaryochloris are the only known oxyphototrophs that have exchanged chlorophyll a (Chl a) with Chl d as their primary photopigment, facilitating oxygenic photosynthesis with near infrared (NIR) light. Yet their ecology and natural habitats are largely unknown. We used hyperspectral and variable chlorophyll fluorescence imaging, scanning electron microscopy, photopigment analysis and DNA sequencing to show that Acaryochloris-like cyanobacteria thrive underneath crustose coralline algae in a widespread endolithic habitat on coral reefs. This finding suggests an important role of Chl d-containing cyanobacteria in a range of hitherto unexplored endolithic habitats, where NIR light-driven oxygenic photosynthesis may be significant.     

Cell-free synthesis of functional proteins using transcription/translation machinery entrapped in silica sol-gel matrix

Herewith we report the encapsulation of functional protein synthesis machinery in a silica sol-gel matrix. When the sol-gel reaction using alkoxysilane monomers was carried out in the presence of Escherichia coli cell extract, macromolecular protein synthesis machinery in the cell extract was successfully immobilized within a silica gel matrix, catalyzing the translation of co-immobilized DNA when supplied with small-molecular-weight substrates for protein synthesis. The efficiency of protein synthesis was affected by the pore size of the gel structure, which was controlled through the use of appropriate additives during the sol-gel reactions. To the best of our knowledge, this is the first report describing the reproduction of the entire set of complicated biological process within an inorganic gel matrix, and we expect that the developed technology will find many applications in numerous fields such as high-throughput gene expression and the development of multifunctional biosensors.     

Estimation of photosynthesis in cyanobacteria by pulse-amplitude modulation chlorophyll fluorescence: problems and solutions

Cyanobacteria are photosynthetic prokaryotes and widely used for photosynthetic research as model organisms. Partly due to their prokaryotic nature, however, estimation of photosynthesis by chlorophyll fluorescence measurements is sometimes problematic in cyanobacteria. For example, plastoquinone pool is reduced in the dark-acclimated samples in many cyanobacterial species so that conventional protocol developed for land plants cannot be directly applied for cyanobacteria. Even for the estimation of the simplest chlorophyll fluorescence parameter, F _v/F _m, some additional protocol such as addition of DCMU or illumination of weak blue light is necessary. In this review, those problems in the measurements of chlorophyll fluorescence in cyanobacteria are introduced, and solutions to those problems are given.     

Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp.PCC 6803

Protein lysine methylation is a prevalent post-translational modification (PTM) and plays critical roles in all domains of life. However, its extent and function in photosynthetic organisms are still largely unknown. Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation. Here we integrated propionylation of monomethylated proteins, enrichment of the modified peptides, and mass spectrometry (MS) analysis to identify monomethylated proteins in Synechocystis sp. PCC 6803 (Synechocystis). Overall, we identified 376 monomethylation sites in 270 proteins, with numerous monomethylated proteins participating in photosynthesis and carbon metabolism. We subsequently demonstrated that CpcM, a previously identified asparagine methyltransferase in Synechocystis, could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480. The loss of CpcM led to decreases in the maximum quantum yield in primary photosystem II (PSII) and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis. We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria. The large number of monomethylated proteins and the identification of CpcM as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.     

Chilean high-altitude hot-spring sinters: a model system for UV screening mechanisms by early Precambrian cyanobacteria

Before the build‐up of stratospheric ozone, Archean and early Proterozoic phototrophs existed in an environment subjected to highly elevated levels of ultraviolet (UV) radiation. Therefore, phototrophic life would have required a protective habitat that balanced UV attenuation and photosynthetically active radiation (PAR) transmission. Here we report on aspects of the phototroph geomicrobiology of El Tatio geothermal field, located at 4300 m in the Andes Mountains of northern Chile (22 °S), as an analogue system to early Precambrian environments. El Tatio microbes survive in a geochemical environment of rapidly precipitating amorphous silica (sinter) and unusually high solar radiation (including elevated UV‐B flux) due to the high‐altitude, low‐latitude location. Cyanobacteria produce 10‐mm‐thick surface mats containing filaments encased in amorphous silica matrices up to 5 µm thick. Relative radiation absorbance of these silica matrices was UV‐C > UV‐B > UV‐A > PAR, suggesting the silica provides a significant UV shield to the cyanobacteria. Cyanobacteria also occur in cryptoendolithic communities 1–10 mm below siliceous sinter surfaces, and in siliceous stromatolites, where viable cyanobacteria are found at least ～10 mm below the sinter surface. UV‐B was dramatically attenuated within ～1 mm of the sinter surface, whereas UV‐C (a frequency range absent today but present in the early Precambrian) was attenuated even more efficiently. PAR was attenuated the least, and minimum PAR levels required for photosynthesis penetrated 5–10 mm into the sinter. Thus, a favourable niche occurs between approximately 1–10 mm in siliceous sinters where there is a balance between PAR transmission and UV attenuation. These deposits also would have strongly attenuated Archean and early Precambrian levels of UV and thus, by analogy, cyanobacteria of early Precambrian shallow aquatic environments, inhabiting silicified biofilms and silica stromatolites, would have similarly been afforded protection against high‐intensity UV radiation.     

Cell‐mediated deposition of porous silica on bacterial biofilms

Living hybrid materials that respond dynamically to their surrounding environment have important applications in bioreactors. Silica based sol–gels represent appealing matrix materials as they form a mesoporous biocompatible glass lattice that allows for nutrient diffusion while firmly encapsulating living cells. Despite progress in sol–gel cellular encapsulation technologies, current techniques typically form bulk materials and are unable to generate regular silica membranes over complex geometries for large‐scale applications. We have developed a novel biomimetic encapsulation technique whereby endogenous extracellular matrix molecules facilitate formation of a cell surface specific biomineral layer. In this study, monoculture Pseudomonas aeruginosa and Nitrosomonas europaea biofilms are exposed to silica precursors under different acid conditions. Scanning electron microscopy (SEM) imaging and electron dispersive X‐ray (EDX) elemental analysis revealed the presence of a thin silica layer covering the biofilm surface. Cell survival was confirmed 30 min, 30 days, and 90 days after encapsulation using confocal imaging with a membrane integrity assay and physiological flux measurements of oxygen, glucose, and NH. No statistical difference in viability, oxygen flux, or substrate flux was observed after encapsulation in silica glass. Shear induced biofilm detachment was assessed using a particle counter. Encapsulation significantly reduced detachment rate of the biofilms for over 30 days. The results of this study indicate that the thin regular silica membrane permits the diffusion of nutrients and cellular products, supporting continued cellular viability after biomineralization. This technique offers a means of controllably encapsulating biofilms over large surfaces and complex geometries. The generic deposition mechanism employed to form the silica matrix can be translated to a wide range of biological material and represents a platform encapsulation technology. Biotechnol. Bioeng. 2011;108: 2249–2260. © 2011 Wiley Periodicals, Inc.     

Gene-targeted and site-directed mutagenesis of photosynthesis genes in cyanobacteria

This historical minireview traces the development and application of methods for gene-targeted and site-directed mutagenesis of photosynthesis genes in cyanobacteria (mainly Synechocystis sp. PCC 6803). This approach allowed important data to be obtained on the structure and function of Photosystem I and Photosystem II complexes. I describe some of the major contributions of molecular genetics and subsequent mutant analysis in the 1980s and early 1990s that led to substantial advances in our knowledge of basic principles regarding the organization of the photosynthetic apparatus. This molecular-genetic research on cyanobacteria has initiated a fresh wave of photosynthesis research and created a solid foundation for rapid progress at the threshold of the twenty-first century. This revised version was published online in June 2006 with corrections to the Cover Date.     

巢湖蓝藻水华形成原因探索及"优势种光合假说"

为探索蓝藻水华的形成原因,从2007以来对巢湖西区浮游藻类种类、优势种季节变化、初级生产力、水质参数及优势种的光合生理生态学特性作了观测。关于蓝藻水华形成过程中迅猛发展的原因,近80a已提出了10种假说,但对解释巢湖形成的蓝藻水华,尚显不足。本文基于我们对蓝藻水华的了解,提出了如下“优势种光合假说”：（1）蓝藻水华包含各种藻类,蓝藻水华发生不仅与藻细胞浓度有关,还与水体初级生产力直接有关。巢湖中这两者在夏季最大,在冬季最小。但无定量关系。（2）水华藻类中生长最快、细胞密度最大的是优势种,含有多个优势种时可能随季节更替。巢湖几乎整年发生蓝藻水华,已检测出4种优势种都是蓝藻,从早春起先是水华鱼腥藻,以后有绿色微囊藻、惠氏微囊藻和铜绿微囊藻。（3）各种环境因子都影响优势种生长,其中少数主导因子影响较大。在巢湖富营养条件下,光强、温度和pH值是主导因子。（4）主导因子对优势种光合活性的影响,可决定其能否处于优势。巢湖的温度和pH值变化可能促进了惠氏微囊藻取代绿色微囊藻,铜绿微囊藻取代惠氏微囊藻,而光强变化可能调节冬季时水华鱼腥藻取代了绿色微囊藻,春季时正好是相反的取代。     

Diel Migrations of Microorganisms within a Benthic, Hypersaline Mat Community

We studied the diel migrations of several species of microorganisms in a hypersaline, layered microbial mat. The migrations were quantified by repeated coring of the mat with glass capillary tubes. The resulting minicores were microscopically analyzed by using bright-field and epifluorescence (visible and infrared) microscopy to determine depths of coherent layers and were later dissected to determine direct microscopic counts of microorganisms. Microelectrode measurements of oxygen concentration, fiber optic microprobe measurements of light penetration within the mat, and incident irradiance measurements accompanied the minicore sampling. In addition, pigment content, photosynthesis and irradiance responses, the capacity for anoxygenic photosynthesis, and gliding speeds were determined for the migrating cyanobacteria. Heavily pigmented Oscillatoria sp. and Spirulina cf. subsalsa migrated downward into the mat during the early morning and remained deep until dusk, when upward migration occurred. The mean depth of the migration (not more than 0.4 to 0.5 mm) was directly correlated with the incident irradiance over the mat surface. We estimated that light intensity at the upper boundary of the migrating cyanobacteria was attenuated to such an extent that photoinhibition was effectively avoided but that intensities which saturated photosynthesis were maintained through most of the daylight hours. Light was a cue of paramount importance in triggering and modulating the migration of the cyanobacteria, even though the migrating phenomenon could not be explained solely in terms of a light response. We failed to detect diel migration patterns for other cyanobacterial species and filamentous anoxyphotobacteria. The sulfide-oxidizing bacterium Beggiatoa sp. migrated as a band that followed low oxygen concentrations within the mat during daylight hours. During the nighttime, part of this population migrated toward the mat surface, but a significant proportion remained deep.     

The quantitative proteome atlas of a model cyanobacterium

Cyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular localizations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label-free quantitative proteomics, we map 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments and generate a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community.     

Adaptation to Hydrogen Sulfide of Oxygenic and Anoxygenic Photosynthesis among Cyanobacteria

Four different types of adaptation to sulfide among cyanobacteria are described based on the differential toxicity to sulfide of photosystems I and II and the capacity for the induction of anoxygenic photosynthesis. Most cyanobacteria are highly sensitive to sulfide toxicity, and brief exposures to low concentrations cause complete and irreversible cessation of CO₂ photoassimilation. Resistance of photosystem II to sulfide toxicity, allowing for oxygenic photosynthesis under sulfide, is found in cyanobacteria exposed to low H₂S concentrations in various hot springs. When H₂S levels exceed 200 μM another type of adaptation involving partial induction of anoxygenic photosynthesis, operating in concert with partially inhibited oxygenic photosynthesis, is found in cyanobacterial strains isolated from both hot springs and hypersaline cyanobacterial mats. The fourth type of adaptation to sulfide is found at H₂S concentrations higher than 1 mM and involves a complete replacement of oxygenic photosynthesis by an effective sulfide-dependent, photosystem II-independent anoxygenic photosynthesis. The ecophysiology of the various sulfide-adapted cyanobacteria may point to their uniqueness within the division of cyanobacteria.     

Antenna replacement in the evolutionary origin of chloroplasts

The endosymbiotic origin of chloroplasts from unicellular cyanobacteria is presently beyond doubt. Oxygenic photosynthesis is based on coordinated action of the two photosystems (PS), PS I and PS II, cooperating with several variants of the pigment antenna. In cyanobacteria, red algae, and glaucophytes, phycobilisomes (PBS) act as antennae, while in terrestrial plants, as well as in most macro- and microalgae, antennae are formed by chlorophyll a/b- and chlorophyll a/c-containing proteins. Advantages and disadvantages of the PBS antenna compared to other light-harvesting complexes form the basis for adaptive variations of the antenna in the course of development of eukaryotic photosynthesis. During the evolution of the “green” and “chromophyte” lineages of the chloroplasts, PBS, in spite of their optimal features of light absorption, were replaced by chlorophyll a/b- and chlorophyll a/c-containing light-harvesting complexes. Development of the cell wall associated with the limitation of motility and tissue formation in photosynthetic eukaryotes were the factors responsible for the antenna shift. The subsequent redistribution of cell resources in favor of cellulose biosynthesis required for increased CO₂ consumption, higher PS II levels, and greater number and density of the thylakoids in the chloroplasts, was incompatible with the energy-consuming and overly large PBS antenna.     

Action spectra of microalgal photosynthesis and depth distribution of spectral scalar irradiance in a coastal marine sediment of Limfjorden, Denmark

The role of complementary spectral utilization of light for the zonation of different groups of oxygenic phototrophic organisms in sediments was studied. The marine sediment was covered by a dense population of diatoms with an underlying population of cyanobacteria. Action spectra for photosynthesis and spectral scalar irradiance, E₀, were measured directly in the sediment at a spatial resolution of 0.1 mm by the use of oxygen and light microsensors. The action spectrum for the diatoms was similar to the attenuation spectrum of the scalar irradiance, K₀, in the diatom layer with Chl.a. and carotenoids being the major photosynthetic pigments. The action spectrum of the cyanobacteria showed photosynthesis maxima at the absorption regions of Chl.a. and phycocyanin. The measured depth distribution of spectral scalar irradiance and the action spectra of diatoms and cyanobacteria were used to calculate the spectral quality for photosynthesis of the 400–700 nm light to which the two populations were exposed. This spectral quality was compared to that of the light incident on the sediment surface. Due to preferential extinction of wavelengths, at which their photosynthetically active pigments had maximal absorption, the relative light quality for diatoms was reduced to 85% of the quality of d incident light at a similar total quantum flux. This effect was partly due to spectral alterations of light backscattered from the underlying sediment with cyanobacteria. The cyanobacteria at the bottom of the euphotic zone, in contrast, experienced a light spectrum which was favorably altered, to 10% in quality, due to absorption by the overlying diatoms. It was concluded that these changes in spectral light quality can be considered as only one of more factors explaining the zonation of the two phototrophic populations, and that total light intensity and the chemical microenvironment are probably more important factors.     

Epibiosis of Oxygenic Phototrophs Containing Chlorophylls a, b, c, and d on the Colonial Ascidian Cystodytes dellechiajei

The external surfaces of marine animals are colonized by a wide variety of epibionts. Here, we study the phototrophic epibiotic community attached to the colonial ascidian Cystodytes dellechiajei collected in the Mediterranean Sea. Epifluorescence microscopy analysis showed abundant filamentous cyanobacteria on the upper and basal parts of the ascidian that displayed autofluorescence, as well as some unicellular cyanobacteria, diatoms, and structures, which could belong to microscopic rhodophyte algae. In addition, high-performance liquid chromatography of the photosynthetic pigments confirmed that the phototrophic epibionts possess chlorophyll (Chl) d, as well as Chl a, b, and c, which enable them to use far-red light for photosynthesis in that peculiar microenvironment. Furthermore, laser scanning confocal microscopy showed the presence of a few small patches of cells on the basal part of the ascidian displaying fluorescence between 700 and 750?nm after excitement with a 635-nm red laser, typically within the range of Chl d. Denaturing gradient gel electrophoresis of the 16S rRNA gene polymerase chain reaction amplified using specific primers for Cyanobacteria detected sequences related with the genera Planktothricoides, Synechococcus, Phormidium, and Myxosarcina, as well as sequences of chloroplasts of diatoms and rhodophyte algae. Remarkably, only the sequences related to the filamentous cyanobacteria Planktothricoides spp. and some chloroplast sequences were found in almost all specimens collected under different macroecological conditions and geographical areas, suggesting thus certain specificity in the epibiotic association. On the other hand, Prochloron spp. and Acaryochloris marina, typically associated to tropical ascidians, were not detected by denaturing gradient gel electrophoresis. However, given the low abundance of cells displaying Chl d in C. dellechiajei and the fact that molecular fingerprinting techniques not always recover low abundance groups, the presence of these cyanobacteria cannot be ruled out. Nevertheless, our data indicate that tropical ascidians and C. dellechiajei differ in their phototrophic communities, although Chl d-containing cells are present in both microenvironments.     

Collagenolytic activity in several species of deuteromycetes under various storage conditions

The ability of deuteromycetes of the genera Penicillium, Aspergillus, and Botrytis to retain collagenolytic activity was studied after both 2 and 10 years of storage on a Czapek medium under a layer of mineral oil at 4°C, as well as in silica gel granules at 20 and ?60°C. The enzymatic activity of several species, including Botrytis terrestris, Penicillium janthinellum, Penicillium chrysogenum, and Penicillium citrinum, was retained under both conditions of storage. Aspergillus repens retained enzymatic activity only if stored under a layer of mineral oil. The viability of conidia and the collagenolytic activity of Botrytis terrestris, P. janthinellum, P. chrysogenum, and Penicillium citrinum, maintained on silica gel for 10 years, depended on the storage temperature. The viability of the test strains improved after storage on a silica gel at ?60°C. A strain of Aspergillus repens lost its ability to dissolve collagen at various storage tempeatures on the silica gel. The index of lysis for three strains of Penicillium deuteromycetes (Penicillium janthinellum, Penicillium chrysogenum, and Penicillium citrinum) increased after a 10-year storage on silica gel at ?60°C.     

The Formation and Preservation of Synechococcus elongatus Cell Molds in Simulated Silica Sinter: Implications for the Identification of Microfossils

Siliceous sinters that precipitate around modern hot spring systems are able to fossilize the indigenous microbial communities, forming molds that accurately outline the shape of the microorganisms. Over time, the biomass decays, and only silica molds or their infill may remain as evidence of the former living cells. However, little is known regarding the fidelity of such silica molds in terms of size and morphology, and the preservation of critical parameters for the identification of ancient silicified microorganisms by silica molds remains untested. Here we report experiments examining the formation of microbial molds of the cyanobacterium Synechococcus elongatus in silica gel. We demonstrate that post-depositional processes, primarily desiccation, are crucial for obtaining accurate and robust molds, and that initial desiccation acts to strengthen cell molds against further alteration. However, all silica gel treatments systematically created preservational biases (changes in size, additional structures) that may be misleading and may complicate the identification of fossil microorganisms.